Major League Phase
Pick | Player | Position | Drafted By | Drafted From | 2011 Club |
| 1 | Rhiner Cruz | RHP | Houston | New York (NL) | Buffalo |
| 2 | Terry Doyle | RHP | Minnesota | Chicago (AL) | Charlotte |
| 3 | Lucas Luetge | LHP | Seattle | Milwaukee | Nashville |
| 4 | Ryan Flaherty | 2B | Baltimore | Chicago (NL) | Iowa |
| 5* | Cesar Cabral | LHP | Kansas City | Boston | Pawtucket |
| 6 | Lendy Castillo | RHP | Chicago (NL) | Philadelphia | Lehigh Valley |
| 7 | Gustavo Nunez | SS | Pittsburgh | Detroit | Toledo |
| 8 | Robert Fish | LHP | Atlanta | Los Angeles (AL) | Salt Lake |
| 9 | Erik Komatsu | OF | St. Louis | Washington | Syracuse |
| 10** | Marwin Gonzalez | SS | Boston | Chicago (NL) | Iowa |
| 11 | Brett Lorin | RHP | Arizona | Pittsburgh | Indianapolis |
| 12 | Brad Meyers | RHP | New York (AL) | Washington | Syracuse |
Triple-A Phase
Pick | Player | Position | Drafted By | Drafted From | 2010 Club |
| 1*** | Marco Duarte | RHP | Houston | Colorado | Tulsa |
| 2 | Marty Popham | RHP | Minnesota | Cleveland | Akron |
| 3 | Andy Loomis | LHP | Baltimore | Philadelphia | Reading |
| 4 | Thomas Melgarejo | LHP | Kansas City | Los Angeles (NL) | Chattanooga |
| 5 | Ricky Alvarez | 3B | Chicago (NL) | Los Angeles (AL) | Arkansas |
| 6 | Michael Wing | SS | San Diego | Los Angeles (AL) | Arkansas |
| 7 | Aaron Poreda | LHP | Pittsburgh | San Diego | San Antonio |
| 8 | Donnie Webb | OF | Miami | Cleveland | Akron |
| 9 | Travis Mattair | SS | Cincinnati | Philadelphia | Reading |
| 10 | Beau Seabury | C | Washington | Colorado | Tulsa |
| 11 | Javier Avendano | RHP | Toronto | St. Louis | Springfield |
| 12 | Luis Rojas | RHP | San Francisco | New York (NL) | Kingsport |
| 13 | Barret Browning | LHP | St. Louis | Los Angeles (AL) | Arkansas |
| 14 | Gerardo Olivares | C | Boston | Tampa Bay | Montgomery |
| 15 | Domnit Bolivar | SS | Milwaukee | St. Louis | Springfield |
| 16 | Fabian Williamson | LHP | Texas | Oakland | Midland |
| 17 | Francisco Diaz | C | Pittsburgh | Philadelphia | Reading |
| 18 | Gabe Jacobo | OF | Toronto | Los Angeles (AL) | Arkansas |
| 19 | Shooter Hunt | RHP | St. Louis | Minnesota | New Britain |
| 20 | Efrain Nunez | OF | Texas | Seattle | Jackson |
| 21 | Charles Cutler | C | Pittsburgh | St. Louis | Springfield |
| 22 | Hector Alvarez | C | Toronto | New York (NL) | Binghamton |
| 23 | Alexander Buchholz | SS | Texas | Cincinnati | Carolina |
Double-A Phase
Pick | Player | Position | Drafted By | Drafted From | 2010 Club |
| 1 | Matthew Sweeney | 3B | Baltimore | Tampa Bay | Charlotte |
| 2 | Matthew Buschmann | RHP | Washington | San Diego | Lake Elsinore |
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